Restriction enzyme analysis of mitochondrial DNA of members of the genus Aspergillus as an aid in taxonomy

Restriction endonuclease patterns of mitochondrial DNA from seven species of the genus Aspergillus (A. nidulans, A. wentii, A. awamori, A. niger, A. oryzae, A. tamarii and A. echinulatus) have been compared in order to test the phylogenetic relationships between these species. The fraction of restriction fragments common between all pairs of species from this set ranged from 0 to 1. The use of this approach for the taxonomy of the genus Aspergillus is discussed. The postulated phylogenetic relationships differ significantly in two cases from the classification of the genus presented by Raper & Fennell (1965).     

Restriction endonuclease analysis of mitochondrial DNA as an aid in the taxonomy of Naegleria and Vahlkampfia

Using restriction enzyme analysis, mitochondrial DNA fragment patterns from seven strains of pathogenic and nonpathogenic Naegleria and one strain of Vahlkampfia were compared to estimate nucleotide sequence divergence. Significantly high levels of estimated genetic variation between strains of N. gruberi, N. fowleri, and N. jadini support the current taxonomic level of the individual Naegleria species and suggest a distinct phylogeny for each group. Naegleria lovaniensis, strain TS, was shown to have significant nucleotide sequence homology with N. gruberi, strain EGs, suggesting that the two groups share a close taxonomic relationship. The pathogenic strain MB-41 of N. fowleri exhibited distinct genetic divergence from the highly homologous, pathogenic strain Nf66 and the drug-cured strain 6088. Morphologically distinct strains EGs and 1518/la of N. gruberi exhibited significantly large sequence divergence consistent with a more distant taxonomic relationship. Amoebae from the genus Vahlkampfia expressed genetic similarity with strains of N. gruberi.     

Restriction enzyme analysis of mitochondrial DNA of Acanthamoeba strains in Japan

Eight isolates, identified as either Acanthamoeba castellanii or A. polyphaga from human eye infections, contact lens containers, and soil in Japan, were characterized by restriction fragment length polymorphisms (RFLP) of mitochondrial DNA (mtDNA). Mitochondrial DNA was digested with either Bgl II, EcoR I, Hind III, Hpa I, Sca I or Xba I, electrophoresed in agarose gels, and stained with ethidium bromide. Four distinct RFLP phenotypes that refer to the collection of six fragment size patterns obtained for a single strain with six enzymes, were discovered among the eight strains used in this study. Three strains morphologically classified as A. polyphaga share a single RFLP phenotype with the Ma strain of A. castellanii. The interspecific sequence differences of 7.06-12.74% in DNA nucleotide were estimated from the proportion of DNA fragments shared by each pair of mtDNA.     

Restriction enzyme analysis of mitochondrial DNA in colorectal tumours.

Total cellular DNA samples were isolated from 15 colorectal adenocarcinomas, 8 colon adenomas and their adjacent histologically normal colon mucosa. These DNA samples were digested separately with 13 different restriction endonucleases and analysed by Southern blot hybridization using a purified 32P-labelled human mtDNA probe. The fragment patterns from tumour mtDNA were compared to those from corresponding normal mtDNA. No evidence for large deletions, insertions, rearrangements or single base mutations in the detectable regions was detected. This suggests that other mechanisms may be responsible for the changes of colorectal tumour mitochondria.     

Restriction enzyme analysis of variation and taxonomy in the kelp genus Laminaria (Laminariales,Phaeophyta)

High levels of phenotypic variation in kelp species necessitate the use of taxonomic markers that are independent of morphology. Restriction fragment length polymorphism (RFLP) analysis of nuclear DNA can provide such markers. In this paper we present the results of an RFLP analysis of cytoplasmic ribosomal DNA (rDNA) in three Laminaria species (L. agardhii, L. digitata, L. groenlandica). Comparison of the restriction maps of the nontranscribed spacer (NTS) in the rDNAs suggests that this method should be useful for the differentiation of these taxa. These results are discussed, as are the applications of RFLP mapping to the identification of field-collected, morphologically variable plants.     

Restriction fragment length polymorphisms in mitochondrial DNA and ribosomal RNA gene complexes as an aid to the characterization of species and sub-species populations in the genus Verticillium

Abstract Genomic DNA was extracted from seven species of Verticillium and digested with the restriction endonucleases Eco RI or Hae III. Hybridization with an homologous V. albo-atrum ribosomal RNA gene probe revealed restriction fragment length polymorphisms (RFLPs) which could differentiate V. lateritium, V. lecanii, V. nigrescens, V. nubilum and V. tricorpus . Digestion with Eco RI did not provide RFLPs which could distinguish between V. albo-atrum and V. dahliae . Digestion of genomic and mitochondrial DNA with Hae III showed distinctive patterns on ethidium bromide gels which allowed each species to be distinguished. Some intra-species variation in patterns occurred and a combination of mitochondrial and ribosomal RNA gene complex RFLPs has potential as an aid for the characterization of species and sub-species populations in the genes Verticillium .     

Restriction enzyme analysis of the Plasmid ColIb DNA

Summary Plasmid ColIb (61.5 Mdal) was digested with restriction enzymes EcoRI and HindIII. The DNA digestion products were separated by electrophoresis on 1.2% agarose gels. There were identified 22 fragments of ColIb DNA generated by the endonuclease EcoRI and 21 fragments produced by HindIII. Molecular weights of the fragments were estimated. The total molecular weight of the fragments generated by EcoRI was 61.42 Mdal and for HindIII fragments 62.79 Mdal.     

Comparative restriction enzyme analysis of mitochondrial DNA in several populations of lake resident chars of the genus Salvelinus

Restriction enzyme analysis was employed in studying the mitochondrial DNA (mtDNA) ATPase6/ND4L region in several Northeast Asian populations of resident lake char of the genus Salvelinus. On evidence of mitotypes, genetic similarity was assumed for populations of neiva (Ueginskoe Lake), lake resident char from the northern coast of the Sea of Okhotsk (Mak-Mak Lake and Elekchanskie lakes), and dolly varden. Mitotype AAAA proved to be common for these populations. Lake char populations of the Juliet and Maxi lakes (the basin of the Kolyma river) had mitotype DBAA, which is similar to mitotype DBAB observed earlier in Taranetz char S. taranetzi from Chukotka. The divergence between mitotypes AAA and DBAA was estimated at 0.3%. Different origins were assumed for the lake resident char populations from the basins of the Sea of Okhotsk and of the Kolyma River, the former originating in the Pacific and the latter, in the Arctic basins.     

Restriction enzyme analysis of tomato chloroplast and chromoplast DNA

Plastid DNA was isolated from the chloroplasts of tomato (Lycopersicon esculentum var Traveler 76) leaves and the chromoplasts of ripe tomato fruit. Comparisons of the two DNAs were made by restriction endonuclease analysis using PvuII, HpaI, and Bg1I. No differences in the electrophoretic banding patterns of the restricted plastid DNAs were detected, indicating that no major rearrangements, losses, or gains of plastid DNA accompany the transition from chloroplast to chromoplast.     

Root peroxidase isoenzymes as an aid in Citrus breeding and taxonomy

Summary A rapid method for differentiating between Citrus clones as well as between zygotic and nucellar plants has been developed. It is based on determination of peroxidase isoenzyme patterns in small root samples. Ten to 14 bands could be distinguished, in contrast to the small number of bands present in leaves. Tetraploid seedlings gave uniform patterns closely resembling the diploid, while triploids showed segregation in isozyme pattern.Contribution from the Agricultural Research Organization, The Volcani Center, Bet Dagan (Israel).This research was supported by the U.S.-Israel Binational Science Foundation, Grant No. 204/020.     

Restriction enzyme analysis of satellite DNA components from the bovine genome

A restriction enzyme analysis was performed on satellite DNA components, isolated, as described in the preceding paper, from the bovine genome by a combination of Cs2SO4/BAMD and Cs2SO4/Ag+ density gradient centrifugation. Such an analysis has led to the unambiguous identification of eight satellite DNA components and to new information on their repeat units; this indicates that identical repeat lengths are shared by them, a fact strongly suggesting a common origin.     

Restriction Enzyme Analysis of Mitochondrial DNA of Acanthamoeba Strains in Japan

ABSTRACT. Eight isolates, identified as either Acanthamoeba castellanii or A. polyphaga from human eye infections, contact lens containers, and soil in Japan, were characterized by restriction fragment length polymorphisms (RFLP) of mitochondrial DNA (mtDNA). Mitochondrial DNA was digested with either Bgl II, Eco R I, Hind III, Hpa I, Sca I or Xba I, electrophoresed in agarose gels, and stained with ethidium bromide. Four distinct RFLP phenotypes that refer to the collection of six fragment size patterns obtained for a single strain with six enzymes, were discovered among the eight strains used in this study. Three strains morphologically classified as A. polyphaga share a single RFLP phenotype with the Ma strain of A. castellanii. The interspecific sequence differences of 7.06–12.74% in DNA nucleotide were estimated from the proportion of DNA fragments shared by each pair of mtDNA.     

Restriction enzyme analysis of Bacillus subtilis bacteriophage phi 105 DNA

The recognition sites on phi 105 DNA for the restriction endonucleases EcoRI, Bg/II, SmaI, KpnI, SstI, SalI, XhoI, NcoI, PstI, HindIII, ClaI, EcoRV and MluI have been mapped. The sites for EcoRI are shown to be different from those published earlier. The DNA from phi 105 contains no recognition sites for the endonucleases BamHI and XbaI.     

Restriction enzyme analysis of the germ line limited DNA of Ascaris suum

The germ line limited DNA of Ascaris suum was isolated from sperm and testis as a satellite DNA component in Hoechst 33258 — CsCl gradients. Employing restriction enzyme analysis, we show that the germ line limited DNA is composed entirely of two families of tandemly repeated sequences, one repeat unit is 125 bp, and the other 131 bp long. The total appr. 5 × 10⁵ copies of the two families are physically separated from each other (segmental arrangement). Several repeat unit variants within both families could be detected. The copies of sequence variants are arranged in tandem (subsegmental arrangement). Reassociation and hybridization experiments revealed similar sequences of the two repeat units. The archaeotypic core sequence of both repeat units is probably a tetranucleotide which shows a theme and variation pattern. During chromatin diminution in the presoma cells the satellite DNA is eliminated from the chromosomes. However, a limited number of tandemly repeated copies of both kinds of repeat units could be detected in the soma genome using radioactive probes of both repeat units in Southern blots of muscle and intestine of adult animals. The tandem arrangement and the hierarchical pattern of restriction sites throughout different subfamilies supports the model of successive segmental amplification events during the evolution of the germ line limited DNA. Since the germ line limited satellite DNA is exclusively located at the ends of the chromosomes, a fold back structure for the telomeric DNA sequences is proposed which might have generated this DNA.     

Adsorbent polystyrene as an aid in plant enzyme isolation

Porous polystyrene (Amberlite XAD-4) adsorbs hydrophobic and surface-active materials from plant extracts and homogenates. With conventional extraction techniques, these materials tend to bind to proteins by hydrophobic interactions. In some cases covalent modification of protein also occurs. Interfering compounds include phenolics, quinones, terpenes and organic isothiocyanates. Polystyrene complements insoluble polyvinylpyrrolidone (PVPP, Polyclar AT), and the combination of these two adsorbents produced superior enzyme extracts from the several plant tissues that were tested. Tested procedures are described, and suggestions are given for adapting the procedures to new plant systems with contaminating natural products varying in quantity and in chemical nature.     

DNA polymorphism in the Mongolian population. Restriction fragment length polymorphism analysis of mitochondrial DNA]

Restriction enzyme fragment patterns in the D loop and deletion-insertion polymorphism in the V noncoding region of human mitochondrial DNA (mt DNA) were analysed in Mongolian population using the polymerase chain reaction. Polymorphisms were detected and mt DNAs classified into 40 types using seven enzymes--AvaII, BamHI, CfrI131, KpnI, EcoRV, HaeIII RsaI and Asian specific deletion and insertion. The allele frequencies of the polymorphisms and gene diversity were determined. The data obtained for Mongolian population and the literature data were comparatively studied.